chr8-94499376-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 3P and 2B. PM2PP2BP4_Moderate
The NM_015496.5(VIRMA):c.4228A>G(p.Ile1410Val) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000143 in 1,399,928 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 17/23 in silico tools predict a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_015496.5 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
VIRMA | NM_015496.5 | c.4228A>G | p.Ile1410Val | missense_variant, splice_region_variant | 17/24 | ENST00000297591.10 | |
VIRMA | XM_047421677.1 | c.3223A>G | p.Ile1075Val | missense_variant, splice_region_variant | 18/25 | ||
VIRMA | XM_047421678.1 | c.3223A>G | p.Ile1075Val | missense_variant, splice_region_variant | 13/20 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
VIRMA | ENST00000297591.10 | c.4228A>G | p.Ile1410Val | missense_variant, splice_region_variant | 17/24 | 1 | NM_015496.5 | P1 | |
VIRMA | ENST00000521080.5 | n.1843A>G | non_coding_transcript_exon_variant | 6/10 | 1 | ||||
VIRMA | ENST00000522263.5 | c.2157-2896A>G | intron_variant, NMD_transcript_variant | 1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD4 exome AF: 0.00000143 AC: 2AN: 1399928Hom.: 0 Cov.: 27 AF XY: 0.00000288 AC XY: 2AN XY: 694746
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | May 01, 2022 | VIRMA: PM2, BP4 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at